NAME

       Bio::Map::Marker - An central map object representing a generic marker that can have
       multiple location in several maps.

SYNOPSIS

         # get map objects somehow

         # a marker with complex localisation
         $o_usat = Bio::Map::Marker->new(-name=>'Chad Super Marker 2',
                                         -positions => [ [$map1, $position1],
                                                         [$map1, $position2]
                                                       ] );

         # The markers deal with Bio::Map::Position objects which can also
         # be explicitly created and passed on to markers as an array ref:
         $o_usat2 = Bio::Map::Marker->new(-name=>'Chad Super Marker 3',
                                         -positions => [ $pos1,
                                                         $pos2
                                                       ] );

         # a marker with unique position in a map
         $marker1 = Bio::Map::Marker->new(-name=>'hypervariable1',
                                          -map => $map1,
                                          -position => 100
                                          );

         # another way of creating a marker with unique position in a map:
         $marker2 = Bio::Map::Marker->new(-name=>'hypervariable2');
         $map1->add_element($marker2);
         $marker2->position(100);

         # position method is a short cut for get/setting unique positions
         # which overwrites previous values
         # to place a marker to other maps or to have multiple positions
         # for a map within the same map use add_position()

         $marker2->add_position(200);  # new position in the same map
         $marker2->add_position($map2,200); # new map

         # setting a map() in a marker or adding a marker into a map are
         # identical mathods. Both set the bidirectional connection which is
         # used by the marker to remember its latest, default map.

         # Regardes of how marker positions are created, they are stored and
         # returned as Bio::Map::PositionI objects:

         # unique position
         print $marker1->position->value, "\n";
         # several positions
         foreach $pos ($marker2->each_position($map1)) {
            print $pos->value, "\n";
         }

       See Bio::Map::Position and Bio::Map::PositionI for more information.

DESCRIPTION

       A Marker is a Bio::Map::Mappable with some properties particular to markers.  It also
       offers a number of convienience methods to make dealing with map elements easier.

FEEDBACK

   Mailing Lists
       User feedback is an integral part of the evolution of this and other Bioperl modules. Send
       your comments and suggestions preferably to the Bioperl mailing list.  Your participation
       is much appreciated.

         bioperl-l@bioperl.org                  - General discussion
         http://bioperl.org/wiki/Mailing_lists  - About the mailing lists

   Support
       Please direct usage questions or support issues to the mailing list:

       bioperl-l@bioperl.org

       rather than to the module maintainer directly. Many experienced and reponsive experts will
       be able look at the problem and quickly address it. Please include a thorough description
       of the problem with code and data examples if at all possible.

   Reporting Bugs
       Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their
       resolution. Bug reports can be submitted via the web:

         https://github.com/bioperl/bioperl-live/issues

AUTHOR - Chad Matsalla

       Email bioinformatics1@dieselwurks.com

CONTRIBUTORS

       Heikki Lehvaslaiho heikki-at-bioperl-dot-org Lincoln Stein      lstein@cshl.org Jason
       Stajich      jason@bioperl.org Sendu Bala         bix@sendu.me.uk

APPENDIX

       The rest of the documentation details each of the object methods.  Internal methods are
       usually preceded with a _

   new
        Title   : new
        Usage   : my $marker = Bio::Map::Marker->new( -name => 'Whizzy marker',
                                                         -position => $position);
        Function: Builds a new Bio::Map::Marker object
        Returns : Bio::Map::Marker
        Args    :
                  -name    => name of this microsatellite
                              [optional], string,default 'Unknown'
                  -default_map => the default map for this marker, a Bio::Map::MapI
                  -position => map position for this marker, a Bio::Map::PositionI
                  -positions => array ref of Bio::Map::PositionI objects

                  position and positions can also take as values anything the
                  corresponding methods can take

   default_map
        Title   : default_map
        Usage   : my $map = $marker->default_map();
        Function: Get/Set the default map for the marker.
        Returns : L<Bio::Map::MapI>
        Args    : [optional] new L<Bio::Map::MapI>

   map
        Title   : map
        Function: This is a synonym of the default_map() method

                          *** does not actually add this marker to the map! ***

        Status  : deprecated, will be removed in next version

   get_position_object
        Title   : get_position_class
        Usage   : my $position = $marker->get_position_object();
        Function: To get an object of the default Position class
                  for this Marker. Subclasses should redefine this method.
                  The Position returned needs to be a L<Bio::Map::PositionI> with
                          -element set to self.
        Returns : L<Bio::Map::PositionI>
        Args    : none for an 'empty' PositionI object, optionally
                  Bio::Map::MapI and value string to set the Position's -map and -value
                  attributes.

   position
        Title   : position
        Usage   : my $position = $mappable->position();
                          $mappable->position($position);
        Function: Get/Set the Position of this Marker (where it is on which map),
                  purging all other positions before setting.
        Returns : L<Bio::Map::PositionI>
        Args    : Bio::Map::PositionI
                   OR
                  Bio::Map::MapI AND
                  scalar
                   OR
                  scalar, but only if the marker has a default map

   add_position
        Title   : add_position
        Usage   : $marker->add_position($position);
        Function: Add a Position to this marker
        Returns : n/a
        Args    : Bio::Map::PositionI
                   OR
                  Bio::Map::MapI AND
                  scalar
                   OR
                  scalar, but only if the marker has a default map

   positions
        Title   : positions
        Usage   : $marker->positions([$pos1, $pos2, $pos3]);
        Function: Add multiple Bio::Map::PositionI to this marker
        Returns : n/a
        Args    : array ref of $map/value tuples or array ref of Bio::Map::PositionI

   in_map
        Title   : in_map
        Usage   : if ( $marker->in_map($map) ) {}
        Function: Tests if this marker is found on a specific map
        Returns : boolean
        Args    : a map unique id OR Bio::Map::MapI